MolNFT v1 · #184038 · protein

Crystal structure of the human vh antibody domain HEL4

7OBF: “Crystal structure of the human vh antibody domain HEL4”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.62). MolNFT v1 #184038 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7OBF
Type: protein
Length: 245 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HEL4
Ligands: SO4
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HEL4	protein	125	2% helix, 49% strand	—
B	HEL4	protein	120	3% helix, 54% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.62	0.89	26	empty
2	90	0.33	0.73	19	GOL
3	57	0.26	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 911 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7OBF · Crystal structure of the human VH antibody domain HEL4 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7OBF · PDBe 7OBF

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